allocate.mate.ped: allocate.mate.ped
In mghamilton/AllocateMate: An R package for mate allocation
View source: R/allocate.mate.ped.R
allocate.mate.ped R Documentation
allocate.mate.ped
Description
This function generates a mating list for a set of parents.
The mating list can be generated i) to minimise the average inbreeding coefficient (F) of families generated or ii) according to assortative mating principles.
Inputs include a list of parents and a 3-column pedigree file specifying the ancestry of these candidates.
Usage
allocate.mate.ped(ped, parents, max_F = 1, method = "min_F", n_fam_crosses = 1)
Arguments
ped
is a 3-column data frame with the following columns (class in parentheses):
'ID' is the individual identifier of parents and their ancestors (character).
'DAM' is the identifier of the individual's dam (NA if unknown) (character).
'SIRE' is the identifier of the individual's sire (NA if unknown) (character).
parents
data frame with the following columns (class in parentheses):
'ID' is the individual identifier (character).
'SEX' is the sex of the individual - 'M' or 'F', for male and female respectively (character).
'EBV' Estimated breeding value (EBV) of the individual - can not be NA if applying assortative mating as the method (numeric).
'N_AS_PARENT' The number of families the indivdiual is to contribute to. Can be zero if backup parents are to be included in the mating list output (integer).
'FAM' is the full-sibling family identifier. This column may be omitted (character).
max_F
is the maximum inbreeding coefficient allowed in the offspring of parents (numeric between 0 and 1)
method
either 'min_F' (to minimise the average inbreeding in offspring) or 'assortative' (to apply assortative mating) (character)
n_fam_crosses
is the maximum number of siblings from one family allowed to be crossed with siblings of another family. This represents a constraint on the generation of 'double first cousins'. (integer)
Value
'summary' is a data frame containing a summary of all possible families generated from crosses between parents:
'SELECTED' N represents unselected families, Y represents selected families (i.e. mate allocations to be generated) and All represents all possible families.
'COUNT_FAMS' count of families.
MEAN_EBV' mean of family EBVs.
'SD_EBV' standard deviation of family EBVs.
'MIN_EBV' minimum of family EBVs.
'MIN_EBV' maximum of family EBVs.
MEAN_EBV' mean of family inbreeding coefficients (F).
'SD_EBV' standard deviation of family inbreeding coefficients (F).
'MIN_EBV' minimum of family inbreeding coefficients (F).
'MIN_EBV' maximum of family inbreeding coefficients (F).
'all_families' is a data frame containing details of all possible families able to be generted from matings between parents:
'SIRE' male parent.
'DAM' female parent.
'F' inbreeding coefficient of family members (i.e. the 'family F').
'EBV' mean of parent EBVs (i.e. the 'family EBV').
'SELECTED' N represents an unselected family (i.e. family is not to be generated), Y represents a selected family (i.e. mate allocated - family to be generated).
'optimal_families' is a data frame containing details of mate allocations (i.e.families to be generated from matings between parents):
'SIRE' male parent.
'DAM' female parent.
'F' inbreeding coefficient of family members (i.e. expected inbreeding in progeny).
'EBV' mean of the selected parent EBVs (i.e. expected EBV of progeny).
'mating_list' is a data frame containing details of mate allocations including potential replacement individuals:
'CROSS' computer generated cross (progeny family) identifier.
'SIRE' 'Selected' or 'Backup' male parent.
'SIRE_EBV' estimated breeding value (EBV) of the sire.
'SIRE_FAM' full-sibling family identifier of the sire. Computer generated if the FAM column is omitted from 'parents'.
'SIRE_RANK' rank of sire within SIRE_FAM based on SIRE_EBV.
'SIRE_CATEGORY' either 'Selected' (i.e. N_AS_PARENT > 0 in 'parents'), or a 'Backup' (i.e. N_AS_PARENT = 0 in 'parents') that could replace the selected sire in the CROSS.
'DAM' 'Selected' or 'Backup' female parent.
'DAM_EBV' estimated breeding value (EBV) of the dam.
'DAM_FAM' full-sibling family identifier of the dam. Computer generated if the FAM column is omitted from 'parents'.
'DAM_RANK rank of the dam within DAM_FAM based on DAM_EBV.
'DAM_CATEGORY' either 'Selected' (i.e. N_AS_PARENT > 0 in 'parents'), or a 'Backup' (i.e. N_AS_PARENT = 0 in 'parents') that could replace the selected dam in the CROSS.
'F' expected inbreeding coefficient for the progeny of the cross.
'EBV' mean of the selected parent EBVs (i.e. expected EBV of progeny).
'CROSSES_WITH_SIRE_FAM list of CROSS containing a sire or dam from the same family as the sire.
'CROSSES_WITH_DAM_FAM list of CROSS containing a sire or dam from the same family as the dam.
'A_matrix' relationship matrix (numerator relationship matrix; NRM) for 'Selected' parents.
Examples
#Retrieve example data
ped <- AllocateMate::ped
parents <- AllocateMate::parents
output <- allocate.mate.ped(ped, parents, max_F = 0.02, method = "min_F", n_fam_crosses = 1)
output$summary
head(output$all_families)
head(output$optimal_families)
head(output$mating_list)
head(output$A_matrix)
mghamilton/AllocateMate documentation built on Jan. 30, 2025, 6:09 p.m.
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View source: R/allocate.mate.ped.R
| allocate.mate.ped | R Documentation |
allocate.mate.ped
Description
This function generates a mating list for a set of parents. The mating list can be generated i) to minimise the average inbreeding coefficient (F) of families generated or ii) according to assortative mating principles. Inputs include a list of parents and a 3-column pedigree file specifying the ancestry of these candidates.
Usage
allocate.mate.ped(ped, parents, max_F = 1, method = "min_F", n_fam_crosses = 1)
Arguments
ped |
is a 3-column data frame with the following columns (class in parentheses):
|
parents |
data frame with the following columns (class in parentheses):
|
max_F |
is the maximum inbreeding coefficient allowed in the offspring of parents (numeric between 0 and 1) |
method |
either 'min_F' (to minimise the average inbreeding in offspring) or 'assortative' (to apply assortative mating) (character) |
n_fam_crosses |
is the maximum number of siblings from one family allowed to be crossed with siblings of another family. This represents a constraint on the generation of 'double first cousins'. (integer) |
Value
'summary' is a data frame containing a summary of all possible families generated from crosses between parents:
'SELECTED' N represents unselected families, Y represents selected families (i.e. mate allocations to be generated) and All represents all possible families.
'COUNT_FAMS' count of families.
MEAN_EBV' mean of family EBVs.
'SD_EBV' standard deviation of family EBVs.
'MIN_EBV' minimum of family EBVs.
'MIN_EBV' maximum of family EBVs.
MEAN_EBV' mean of family inbreeding coefficients (F).
'SD_EBV' standard deviation of family inbreeding coefficients (F).
'MIN_EBV' minimum of family inbreeding coefficients (F).
'MIN_EBV' maximum of family inbreeding coefficients (F).
'all_families' is a data frame containing details of all possible families able to be generted from matings between parents:
'SIRE' male parent.
'DAM' female parent.
'F' inbreeding coefficient of family members (i.e. the 'family F').
'EBV' mean of parent EBVs (i.e. the 'family EBV').
'SELECTED' N represents an unselected family (i.e. family is not to be generated), Y represents a selected family (i.e. mate allocated - family to be generated).
'optimal_families' is a data frame containing details of mate allocations (i.e.families to be generated from matings between parents):
'SIRE' male parent.
'DAM' female parent.
'F' inbreeding coefficient of family members (i.e. expected inbreeding in progeny).
'EBV' mean of the selected parent EBVs (i.e. expected EBV of progeny).
'mating_list' is a data frame containing details of mate allocations including potential replacement individuals:
'CROSS' computer generated cross (progeny family) identifier.
'SIRE' 'Selected' or 'Backup' male parent.
'SIRE_EBV' estimated breeding value (EBV) of the sire.
'SIRE_FAM' full-sibling family identifier of the sire. Computer generated if the FAM column is omitted from 'parents'.
'SIRE_RANK' rank of sire within SIRE_FAM based on SIRE_EBV.
'SIRE_CATEGORY' either 'Selected' (i.e. N_AS_PARENT > 0 in 'parents'), or a 'Backup' (i.e. N_AS_PARENT = 0 in 'parents') that could replace the selected sire in the CROSS.
'DAM' 'Selected' or 'Backup' female parent.
'DAM_EBV' estimated breeding value (EBV) of the dam.
'DAM_FAM' full-sibling family identifier of the dam. Computer generated if the FAM column is omitted from 'parents'.
'DAM_RANK rank of the dam within DAM_FAM based on DAM_EBV.
'DAM_CATEGORY' either 'Selected' (i.e. N_AS_PARENT > 0 in 'parents'), or a 'Backup' (i.e. N_AS_PARENT = 0 in 'parents') that could replace the selected dam in the CROSS.
'F' expected inbreeding coefficient for the progeny of the cross.
'EBV' mean of the selected parent EBVs (i.e. expected EBV of progeny).
'CROSSES_WITH_SIRE_FAM list of CROSS containing a sire or dam from the same family as the sire.
'CROSSES_WITH_DAM_FAM list of CROSS containing a sire or dam from the same family as the dam.
'A_matrix' relationship matrix (numerator relationship matrix; NRM) for 'Selected' parents.
Examples
#Retrieve example data
ped <- AllocateMate::ped
parents <- AllocateMate::parents
output <- allocate.mate.ped(ped, parents, max_F = 0.02, method = "min_F", n_fam_crosses = 1)
output$summary
head(output$all_families)
head(output$optimal_families)
head(output$mating_list)
head(output$A_matrix)
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